From the Ashes
by wolfsrun
Summary: Kidnapped at birth by Orochimaru in the wake of the Kyuubi attack, Naruto becomes a favored experiment. Watch as he joins a team of fellow experiments who together rise to take on the Elemental Nations. Multi-pairing. Naruto/Naruko/Clone Tsunade.
1. The Serpent and the Beast

**Disclaimer: I do not own Naruto.**

**Chapter 1: The Serpent and the Beast**

The village was in ruins. Fires raged and smoke filled what had once been a cloudless, moonlit night. Cries of pain and screams of rage created a cacophony that pierced the mind and shook the heart. But none of that compared to the bestial roar that drowned out all else.

And yet that roar brought not terror, as it once had, but rather a sense of triumph to the village's survivors. For that roar heralded victory. It was the roar of a monster meeting its doom. It was a roar of loss and pain. But to the villagers it meant life.

What they did not at the time realize was that the roar also meant death. For it was not within the beast to go silently into the night. It demanded that even in victory a price must be paid.

The price paid that night was the life and soul of the Fourth Hokage, Namikaze Minato. The beloved leader of the Village Hidden in the Leaves. And yet, for the beast, that was not enough. In its death throes, it also claimed the life of the Hokage's secret wife, Uzumaki Kushina.

The final moments of the great beast were both horrifying and amazing. And yet, only four individuals were present to witness its end. Two were a young couple of amazing power who would soon be dead. One was a newborn infant who would remember nothing. The last was a small white serpent with an unusual spark of intelligence in its eyes.

The serpent witnessed the beast's end and how the Hokage utilized an intricate seal matrix to split the beast in two. It watched in fascination as half was sealed into the dying Hokage, and the other half into his newborn son.

As the Hokage and his wife breathed their last and the newborn breathed his first as a jinchūriki, the snake decided to take action. It only had moments before the ANBU arrived, but these moments were ones of precious opportunity.

Swiftly, it slithered up to the cooling bodies, and, unhinging its jaw, consumed them both. While this might seem impossible given that the snake was smaller than each of the bodies, the truth was far different. For inside of this serpent, was a pocket dimension. Its belly was actually capable of storing many things for a period of time. Of course, this would be untenable for long term storage, as that would lead to illness. However, for a short period of time, this was a very useful ability.

After consuming the two adults, it quickly moved to the babe and did the same. Its mission accomplished, the snake quickly fled the scene and disappeared into the surrounding woods.

Not a moment later, a squad of ANBU, along with the retired Third Hokage, descended into the clearing. Confusion was paramount as they set about attempting to figure out what happened.

And, as the ANBU floundered about in confusion, and a snake slithered along with smug satisfaction, a babe curled into its dead mother's arms and cried silently.

The date was October 10, 736 Shinobu no Toshi (S.T.), and this incident set in motion a series of events which would forever change the Elemental Nations.

**A/N: Yes, I did just create a dating system for the Naruto Universe. Narutoverse didn't have one, so I figured why not? To give perspective, I am dating 0 S.T. as the year Ōtsutsuki Hagoromo defeated Ōtsutsuki Kaguya. "Shinobu no Toshi" means "Year of the Shinobu" with Shinobu meaning stealth/endure, or recall/remember and is the dictionary form of shinobi. Considering Hagoromo kicked off the era of chakra and ninjas, I felt this was appropriate. Of course, my understanding of Japanese is limited so feel free to point out any errors I may have made. On a side note, I will be using the Japanese style of using family name first and given name second when referring to people. Considering Narutoverse practices a Japanese like culture, I felt this was appropriate. And, if you are wondering why Kushina and Minato did not share a family name, it is because their marriage was done in secret, so they kept their own family names.**


	2. Experiment Report

**Disclaimer: I do not own Naruto.**

**Chapter 2: Experiment Report  
**

**July, 738 Shinobu no Toshi**

Golden eyes with snake-like pupils glowed in the dark as they stared at a computer screen displaying the reports from various experiments.

A chuckle escaped from pale lips as the file of one Mitarashi Anko, designation CS007, was opened up. With deft strokes, the Snake Sannin updated the file to denote a successful experiment followed by the subject's refusal to remain in his services.

It was a shame to lose her so soon, he mused, but as long as she lived there would always be future opportunities to extract more data. It would be interesting to note the long term effects of the experiment on CS007. After all, she was the only survivor of that batch.

Finished with his work, he closed Anko's file and opened the one on subject J009. Uzumaki Naruto. Now here was an interesting subject. It had been nearly two years since his scout had claimed the young jinchūriki for him along with the bodies of his parents. All three had interesting potential, but the jinchūriki made him positively salivate due to his potential. It was a shame that the babe seemed to have suffered some brain damage during the night of the Kyuubi's attack. It seemed some damage had occurred to the babe's prefrontal cortex. While not heavily damaged, this could still result in problems with memory retention, personality expression, moderating social behavior, planning, and decision making. On the plus side, the influx of the Kyuubi's chakra seemed to have accelerated many of the child's body's functions. This included the rate at which the jinchūriki's synapses fired and his nerves transferred signals. Basically, while the child may end up stupid and socially inept, he would have incredible reaction times and be able to make near instantaneous decisions when under pressure. Hypothetically at least.

Of course, there was nothing a little experimentation couldn't fix. He still had the perfectly preserved bodies of the brat's parents. Maybe a little operation was in order? Hmm…

With a few strokes of the keyboard, the Sannin made a reminder for an operation when the child's body grew enough to handle what he had in mind. It was good to get things like this done while the body was still young and malleable. Still, it had to reach a certain threshold before an operation of this nature was even possible.

In the meantime, going over J009's file was giving him some ideas…

"Orochimaru-sama! Subject XG209 is exhibiting signs of instability!"

Orochimaru looked at his subordinate with apathy.

"Dispose of it. I have a more interesting project now anyways."

With a dark chuckle, Orochimaru licked his lips in anticipation. This could turn out to be _very_ interesting.

* * *

**September, 738 Shinobu no Toshi**

It had taken some time to track down Tsunade, but in the end she was somewhat predictable in her habits, so the task was not insurmountable.

He eventually came across her in a small gambling town passed out and being carried back from a bar by her apprentice Shizune. Orochimaru silently stalked them back to their apartment and waited until they were both asleep. It was obvious that they had let their security and situational awareness lax after being off active duty for several years.

After both women were asleep, a quick paralytic toxin in the air made sure they would not react to any stimuli while he went about his business.

It was fortunate that Tsunade was dead to the world, because if she ever found out what he was doing he was fairly certain he would become dead to the world in a more permanent fashion.

Carefully stripping off her sleepwear, Orochimaru picked Tsunade up and placed her on a tarp he had prepared. After all, there would undoubtedly be blood and he didn't want to leave any evidence of his presence.

With a delicate incision into Tsunade's pelvis, he peeled back the flesh to expose the ovaries. And promptly he released a sigh of relief. His entire plan hinged on Tsunade still having eggs in her ovaries. Due to her Creation Rebirth technique which hastened her aging he was worried she might have already entered menopause, thus rendering his efforts futile.

Fortunately, this was not so. There were still some eggs left to her and he set about harvesting every single one with glee. Looks like Tsunade's going to enter menopause early after all! The Snake Sannin chuckled gleefully as he set about his grisly task. Soon he had the eggs safely stored and sealed away.

After cleaning up after himself, erasing the signs of his presence, and taking a large blood sample just for the hell of it, Orochimaru left with none ever being the wiser.

* * *

**November, 738 Shinobu no Toshi**

2342.

That's the number of eggs, or ovarian follicles, Tsunade had left. That means she had only two, maybe three menstruations left. He had cut it close, but in the end his mission was successful.

Unfortunately, that was just the beginning.

Taking some of Senju Hashirama's DNA, which he had in storage, and his sample of Tsunade's blood be began to play around.

Creating various DNA cocktails by splicing these two sources together in varying degrees, he then took the created cells and withdrew their nuclei.

Next, he injected the various nuclei into Tsunade's eggs which he had artificially matured. Of course, some of the nuclei were pure Hashirama, and some were pure Tsunade, but the vast majority were a mixture. After all, he had no idea what could constitute a success and he wanted a variety for this experiment.

As he expected, a vast majority of the eggs did not survive the injection. All of his pure Tsunade and pure Hashirama injections died. Only about half survived the initial injection and after shocking those eggs to stimulate division, only 326 remained.

The losses didn't end there. The process of cell division culled a further 90% of the egg population, allowing only 33 to develop into embryos that could be transferred to an artificial uterus.

Still, he now had 33 embryos developing with a mixture of Hashirama and Tsunade's DNA. If any survived, who knew what potential they might possess?

* * *

**9 August, 739 Shinobu no Toshi**

_Report on Project Tsunade Rebirth:_

_Of the original 2342 eggs, only four subjects survived until birth, and of those three were stillborn._

_That leaves subject TR0956 as the sole survivor. She appears to be a healthy baby girl, with traces of Hashirama's DNA. However, she greatly favors Tsunade in both her genetic makeup and her physical appearance. Only time will tell if she has inherited any unique abilities._

_I have decided to name her Senju Tsukiko and opened a file to track the growth of TR0956._

_I can only hope she lives up to the expectations I have for her._

_On an unrelated note, it seems subject J009's neurocranium and brain are at a sufficient state in development to allow the operation I have been planning. I look forward to the results!_

* * *

**10 August, 739 Shinobu no Toshi**

_Report on subject J009:_

_Success! The operation on J009, went absolutely perfect. While the damage to J009's prefrontal cortex was small, the damage existed in several locations. So, I simply excised that entire region of the brain! Since his neurocranium and brain were developed enough I was able to attach his father's prefrontal cortex as a replacement._

_It was fortunate that I recovered his father's body immediately after death and had it perfectly preserved. It required the rejuvenating properties of Hashirama's DNA to combine these two parts of the brain, but in the end it worked._

_The start of the operation required sealing off the Kyuubi's chakra so I could operate without interference. The close match of the father and son's DNA no doubt facilitated the combination, but I believe it was Hashirama's DNA that truly made the difference._

_I wonder if the similarities in Senju and Uzumaki DNA also helped in this. No matter, the end result is what counts and in this, I was successful._

_One unfortunate side-effect is that the strain on the brain required me to completely shut down the rest of J009's body so that no additional stimuli could affect the brain's incorporation of his new prefrontal cortex._

_I have utilized a complex sealing array to place his body in a form of stasis. Essentially his body is in suspended animation while I will keep his brain active with small periodic injections of Hashirama DNA to act as fuel and promote further healing._

_I have no idea how long it will take for his new brain to stabilize to the point I can take him out of this stasis, but it seems like it might be a long way off._

_On a side note, I now have a large brain tissue sample from a Namikaze/Uzumaki hybrid. This could be fun._

* * *

**19 August, 739 Shinobu no Toshi**

_Report on Project Kushina Rebirth:_

_I decided that since I was successful with Project Tsunade Rebirth, why not try and duplicate that process with Uzumaki Kushina? She is, after all, an Uzumaki._

_Kushina possessed not only the famed Uzumaki longevity, but also the unique ability to utilize chakra chains. It seems a waste not to revive that ability if it is possible._

_Harvesting Kushina's body yielded 24,371 undeveloped eggs. _

_I then isolated the Uzumaki DNA from the Namikaze DNA in Naruto's brain cells so I would not weaken the Uzumaki bloodline I am attempting to recreate. Using this DNA, I then proceeded to create DNA cocktails like I did in Project Tsunade Rebirth, but this time with Kushina and Naruto as the parent subjects._

_Unfortunately it seems that the cells retain traces of the Kyuubi's chakra. This has drastically increased the failure rate of the project. Only 1327 survived the fertilization process to be placed into artificial uteruses. I fear that may not be enough to produce a viable offspring with the corrosive influence of the Kyuubi affecting this experiment._

* * *

**12 May, 740 Shinobu no Toshi**

_Report on Project Kushina Rebirth:_

_Six children born. One boy and five girls. Four of the girls showed severe deformities and had to be put down. That leaves a healthy boy and a healthy girl._

_It's obvious that the influence of the Kyuubi's chakra had a negative effect on this experiment. On the plus side, however, this means that the two surviving subjects, KR00032 (the male) and KR19327 (the female) have the benefit of retaining some of that chakra in their system. This should help jump start their chakra reserves which will be a boon._

_I will run further tests to ensure their health before submitting the final report on this project._

* * *

**13 May, 740 Shinobu no Toshi**

_Report on Project Kushina Rebirth:_

_Subject KR00032 turned out to be a failure as well. It was physically fine, but suffered from severe mental retardation and had to be disposed of._

_The project remains a success however due to KR19327._

_I have decided to name her Uzumaki Naruko after her progenitors. She greatly favors Kushina, but there is some of Naruto in there as well. Her eyes, for example, resemble Naruto's. Perhaps that is just the natural blue babies seem to possess though._

_Genetically, she favors Kushina as well, but she is more of a blend of her parent donors than the product of Project Tsunade Rebirth is._

_A fortunate side effect of the Kyuubi's influence showed itself during my in depth scans. It seems KR19327 possesses the same increased synapse firing rate, and nerve signal transference rate as subject J009. As I predicted it also seems to be jump starting her chakra reserves, and her chakra pathways seem to be improved as well. She will never be J009's equal in chakra capacity, but that is to be expected._

_This concludes Project Kushina Rebirth. I am opening up a file on subject KR19327 to track her growth._

* * *

**3 December, 740 Shinobu no Toshi**

_Report on subject J009:_

_It took some time, but his brain has finally stabilized and I was able to remove the seals keeping J009 in stasis._

_He seems to be responding well, but it will take some time for his brain to adjust to the renewed stimuli from his body. I am starting him on a course of physical therapy to help him adjust._

* * *

**16 January, 741 Shinobu no Toshi**

_Report on subject J009:_

_J009 has responded well to therapy, so I decided to incrementally reintroduce the Kyuubi's chakra to his system. I have exchanged the absolute seal on the Kyuubi which I had layered over his eight trigram seal with an adjustable one with a time release. It will slowly degrade over the course of a year until it completely dissipates, leaving only the eight trigram seal._

_This should allow his brain to readjust to the influx of bijuu chakra that it had been separated from for the past year. The rest of his body should be fine since it was in stasis and hasn't changed since he entered it. The brain is the primary reason for this slow reintroduction._

* * *

**30 July, 742 Shinobu no Toshi**

_Report on subject J009:_

_J009 seems to be extremely eager to begin shinobi training. I have placed him with a physical trainer to keep him occupied, but he seems to be excelling in every task. It seems I may have a true prodigy on my hands._

* * *

**21 March, 743 Shinobu no Toshi**

_Report on subject TR0956:_

_TR0956 seems to have become inspired by J009's activities. The two have formed a friendship and seem to motivate each other. I noticed J009 teaching TR0956 some of the things he has learned so I paired them together under J009's instructor._

_KR19327 has taken to following them around and seems to enjoy watching them train. It may not be long before she can begin her training as well._

* * *

**1 June, 744 Shinobu no Toshi**

_Report on subject KR19327:_

_KR19327 has joined J009 and TR0956 in training. While there is an age disparity, it is not all that great. And, given the friendship the three have formed, I feel they will sufficiently motivate each other so that grouping them will not be a detriment._

_In respect to their ages, while J009 was born 10 October, 736, his 1.3 years in stasis makes him physically around 6.25 years old. With TR0956 being roughly 4.75 years old, and KR19327 being a little over 4 years old, I feel that these three are close enough in age to form an effective team._

_Henceforth KR19327, J009, and TR0956 will be grouped into Team Phoenix._

_Their team will be named Phoenix as a tribute to their rebirth. As, in a sense, all three have been reborn thanks to my experiments. _

_I will open up a file for Team Phoenix to monitor their growth as a team._

**A/N: I do not support harming anyone regardless of their physical or mental abilities. This chapter's display of a callous disregard for human life is simply Orochimaru being Orochimaru.**


End file.
